TCGAbiolinks 1.0.10
Antonio Colaprico , Tiago Chedraoui Silva
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 115691 / Revision: 116712 | | Last Changed Date: 2016-04-02 13:54:55 -0700 (Sat, 02 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && mkdir TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_1.0.10.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_1.0.10.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '1.0.10'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.4Mb
sub-directories of 1Mb or more:
R 2.0Mb
data 6.5Mb
doc 5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.heatmap.plus.sm: no visible binding for global variable 'key'
TCGAanalyze_copynumber: no visible binding for global variable
'geneInfo'
colDataPrepare: no visible binding for global variable 'batch.info'
mutation.genes: no visible global function definition for 'data.table'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [135s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 27.83 0.01 27.85
TCGAanalyze_DEA 14.82 0.09 14.91
TCGAanalyze_Filtering 11.06 0.03 11.09
TCGAvisualize_PCA 6.07 0.01 6.09
TCGAanalyze_Normalization 5.97 0.00 5.97
TCGAanalyze_DMR 5.58 0.03 5.62
TCGAanalyze_EAcomplete 5.54 0.02 5.55
TCGAquery 4.51 0.00 9.08
TCGAdownload 3.83 0.23 8.20
TCGAquery_Version 3.26 0.03 7.91
** running examples for arch 'x64' ... [155s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 31.98 0.00 31.98
TCGAanalyze_DEA 14.81 0.03 14.83
TCGAanalyze_Filtering 14.44 0.00 14.44
TCGAvisualize_PCA 8.18 0.00 8.18
TCGAanalyze_Normalization 7.10 0.00 7.10
TCGAanalyze_DMR 7.00 0.05 7.05
TCGAanalyze_EAcomplete 6.48 0.00 6.48
TCGAvisualize_EAbarplot 5.79 0.04 5.82
TCGAquery 4.75 0.00 8.22
TCGAquery_Version 4.07 0.00 9.72
TCGAdownload 3.49 0.39 9.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [41s]
[41s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [45s]
[45s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'TCGAbiolinks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAbiolinks' as TCGAbiolinks_1.0.10.zip
* DONE (TCGAbiolinks)